How Do You Suggest To Enter Gene Mutations In Protege

Question

[aghili.babak]

I am creating an OWL file from Human Genome at run time so I can later open it in Protege. A first problem I saw is that I can't enter something like HIV-1.c.2752A>T" because of that ">" in it., protege says it is an illegal character. What do you suggest to do?

[Pierre Lindenbaum]

how would it be used ? As a Resource or as a Literal ?

[aghili.babak]

Thanks, I don't really know that much the difference between resource or literal . In the "Code" I am passing them as Classes.. in Protege I am creating them as "Class" too, right click on "thing" and adding a class with a name like "HIV-1.c.2752A>T" to it....which gives error.

Answer 1

[Pierre Lindenbaum]

As far as I understand, you're trying to create a class having a URI containing "HIV-1.c.2752A>T". I don't use protege but I think it is a misunderstanding about protege and RDF/OWL.

• You're not creating a class but an instance (individual) of class. "HIV-1.c.2752A>T" is an instance of a class "Variation"
• you need to create to create an ontology describing what is a Variation, or you can use an existing ontology ( see http://bioportal.bioontology.org/ )
• "HIV-1.c.2752A>T" would be part of a text, a label. Not a URI
• The URI would be a unique identifier for this mutation. Something like http://my.database.org/variations/9808912 or nothing (anonymous URI).

A the end, you're expecting something like this:

(...)
<my:Variation rdf:about="&lt;a href=" http:="" my.database.org="" variations="" 9808912"="" rel="nofollow">http://my.database.org/variations/9808912">
  <my:label>HIV-1.c.2752A>T</my:label>
  <my:position>2752</my:position>
   <my:ref>A</my:ref>
   <my:alt>T</my:alt>
</my:Variation>
(...)

[aghili.babak]

Thanks, so if I understand correetly that "HIV-1.c.2752A>T" should be an "Instance" or "individual " of the class that represents it... please correct me if I understood wrong..thanks.

[Pierre Lindenbaum]

yes, you're right.

[Pierre Lindenbaum]

But you cannot use the sentence: "HIV-1.c.2752A>T" as the URI/identifier of the variation. It wouldn't be a valid URI.